[English] 日本語
Yorodumi
- EMDB-7533: Yeast RNA polymerase III elongation complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7533
TitleYeast RNA polymerase III elongation complex
Map data
SampleYeast RNA polymerase III elongation complex
  • (DNA-directed RNA polymerase III subunit ...Polymerase) x 10
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (Transcription factor ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


positive regulation of transposon integration / RNA polymerase III core binding / termination of RNA polymerase III transcription / tRNA 3'-trailer cleavage / transcription initiation from RNA polymerase III promoter / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding ...positive regulation of transposon integration / RNA polymerase III core binding / termination of RNA polymerase III transcription / tRNA 3'-trailer cleavage / transcription initiation from RNA polymerase III promoter / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / transposon integration / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase III activity / general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / RNA polymerase II preinitiation complex assembly / DNA binding, bending / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II transcribes snRNA genes / mRNA Capping / Formation of the Early Elongation Complex / transcription factor TFIID complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / transcription preinitiation complex / RNA polymerase II, core complex / RNA polymerase II core promoter sequence-specific DNA binding / TBP-class protein binding / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription, RNA-templated / single-stranded DNA binding / DNA-binding transcription factor binding / ribosome biogenesis / disordered domain specific binding / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated / chromatin binding / nucleolus / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor TFIIIB component B'', fungi / Myb DNA-binding like / Transcription factor IIIB subunit Brf1 / Transcription factor TFIIIB component B'', Myb domain / Brf1-like TBP-binding domain / Brf1, TBP-binding domain / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC1, N-terminal ...Transcription factor TFIIIB component B'', fungi / Myb DNA-binding like / Transcription factor IIIB subunit Brf1 / Transcription factor TFIIIB component B'', Myb domain / Brf1-like TBP-binding domain / Brf1, TBP-binding domain / DNA-directed RNA polymerase III subunit Rpc31 / DNA-directed RNA polymerase III, subunit Rpc31 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC1, C-terminal / Pol III subunit C11, C-terminal zinc ribbon / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC9 / RPC5 protein / RNA polymerase III subunit Rpc25 / RNA polymerase III subunit RPC82 helix-turn-helix domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 / RNA polymerase Rpc34 subunit / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 / RNA polymerase Rpc34-like / RNA polymerase III Rpc82, C -terminal / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC40 / DNA-directed RNA polymerases I and III subunit AC19 / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / TATA-box binding protein, conserved site / Transcription factor TFIID repeat signature. / Rpb4/RPC9 superfamily / TBP domain superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Cyclin-like superfamily / SANT/Myb domain / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb8 / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb5, C-terminal domain / : / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / C2C2 Zinc finger
Similarity search - Domain/homology
DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / Transcription factor TFIIIB component B'' / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / Transcription factor IIIB 70 kDa subunit / TATA-box-binding protein ...DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC9 / Transcription factor TFIIIB component B'' / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC3 / Transcription factor IIIB 70 kDa subunit / TATA-box-binding protein / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase III subunit RPC7 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHan Y / He Y
Funding support United States, 6 items
OrganizationGrant numberCountry
Northwestern UniversityCornew Innovation Award United States
American Cancer SocietyIRG-15-173-21 United States
Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community TrustCatalyst Award United States
National Science Foundation XSEDE programCHE110042 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110387 United States
National Energy Research Scientific Computing CenterDE-AC02-05CH11231 United States
CitationJournal: Cell Discov / Year: 2018
Title: Structural visualization of RNA polymerase III transcription machineries.
Authors: Yan Han / Chunli Yan / Susan Fishbain / Ivaylo Ivanov / Yuan He /
Abstract: RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre- ...RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.
History
DepositionMar 8, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseAug 22, 2018-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6cnf
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_7533.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 288 pix.
= 339.84 Å
1.18 Å/pix.
x 288 pix.
= 339.84 Å
1.18 Å/pix.
x 288 pix.
= 339.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.096466765 - 0.19697714
Average (Standard dev.)0.0011304178 (±0.0075874296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 339.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z339.840339.840339.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0960.1970.001

-
Supplemental data

-
Sample components

+
Entire Yeast RNA polymerase III elongation complex

EntireName: Yeast RNA polymerase III elongation complex / Number of Components: 23

+
Component #1: protein, Yeast RNA polymerase III elongation complex

ProteinName: Yeast RNA polymerase III elongation complex / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #2: protein, DNA-directed RNA polymerase III subunit RPC1

ProteinName: DNA-directed RNA polymerase III subunit RPC1Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 162.517812 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #3: protein, DNA-directed RNA polymerase III subunit RPC2

ProteinName: DNA-directed RNA polymerase III subunit RPC2Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 129.629383 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #4: protein, DNA-directed RNA polymerases I and III subunit RPAC1

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.732613 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #5: protein, DNA-directed RNA polymerase III subunit RPC9

ProteinName: DNA-directed RNA polymerase III subunit RPC9Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.623123 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #8: protein, DNA-directed RNA polymerase III subunit RPC8

ProteinName: DNA-directed RNA polymerase III subunit RPC8Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.34977 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #10: protein, DNA-directed RNA polymerase III subunit RPC10

ProteinName: DNA-directed RNA polymerase III subunit RPC10Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.525109 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #12: protein, DNA-directed RNA polymerases I and III subunit RPAC2

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.16786 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #14: protein, DNA-directed RNA polymerase III subunit RPC5

ProteinName: DNA-directed RNA polymerase III subunit RPC5Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.178115 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #15: protein, DNA-directed RNA polymerase III subunit RPC4

ProteinName: DNA-directed RNA polymerase III subunit RPC4Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.751469 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #16: protein, DNA-directed RNA polymerase III subunit RPC3

ProteinName: DNA-directed RNA polymerase III subunit RPC3Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.11282 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #17: protein, DNA-directed RNA polymerase III subunit RPC6

ProteinName: DNA-directed RNA polymerase III subunit RPC6Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.17416 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #18: protein, DNA-directed RNA polymerase III subunit RPC7,DNA-directe...

ProteinName: DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed ...Name: DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.299682 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #19: protein, Transcription factor IIIB 70 kDa subunit,TATA-box-bindin...

ProteinName: Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein,Transcription factor IIIB 70 kDa subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.097867 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #20: protein, Transcription factor TFIIIB component B'',Transcription ...

ProteinName: Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B''
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.249742 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #21: nucleic-acid, DNA (79-MER)

nucleic acidName: DNA (79-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DT)(DC)(DA)(DA)(DC)(DA)(DT)(DA)(DT) (DA)(DT)(DT)(DA)(DG)(DT)(DA)(DA)(DT)(DA) (DC)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG)(DT) (DA)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DC)(DA) (DC)(DA)(DA)(DG)(DA)(DT) ...Sequence:
(DT)(DT)(DC)(DA)(DA)(DC)(DA)(DT)(DA)(DT) (DA)(DT)(DT)(DA)(DG)(DT)(DA)(DA)(DT)(DA) (DC)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG)(DT) (DA)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DC)(DA) (DC)(DA)(DA)(DG)(DA)(DT)(DA)(DA)(DA)(DA) (DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DC)(DA)(DA)(DG)(DT)(DT)(DG)(DG) (DT)(DT)(DA)(DA)(DG)(DG)(DC)(DG)(DT)
MassTheoretical: 24.394693 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

+
Component #22: nucleic-acid, DNA (79-MER)

nucleic acidName: DNA (79-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DC)(DG)(DC)(DC)(DT)(DT)(DA)(DA)(DC) (DC)(DA)(DA)(DC)(DT)(DT)(DG)(DG)(DC)(DC) (DA)(DT)(DG)(DG)(DA)(DG)(DT)(DC)(DA)(DT) (DT)(DT)(DT)(DA)(DT)(DC)(DT)(DT)(DG)(DT) (DG)(DT)(DC)(DA)(DC)(DT) ...Sequence:
(DA)(DC)(DG)(DC)(DC)(DT)(DT)(DA)(DA)(DC) (DC)(DA)(DA)(DC)(DT)(DT)(DG)(DG)(DC)(DC) (DA)(DT)(DG)(DG)(DA)(DG)(DT)(DC)(DA)(DT) (DT)(DT)(DT)(DA)(DT)(DC)(DT)(DT)(DG)(DT) (DG)(DT)(DC)(DA)(DC)(DT)(DT)(DT)(DT)(DA) (DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DG)(DT) (DA)(DT)(DT)(DA)(DC)(DT)(DA)(DA)(DT)(DA) (DT)(DA)(DT)(DG)(DT)(DT)(DG)(DA)(DA)
MassTheoretical: 24.301625 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

+
Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 68.9 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 47141
3D reconstructionSoftware: RELION
CTF correction: CTF amplitude correction was performed following 3D auto refinement in relion.
Resolution: 4.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more